Starting phenix.real_space_refine on Tue Mar 3 15:34:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ro0_24584/03_2026/7ro0_24584.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ro0_24584/03_2026/7ro0_24584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ro0_24584/03_2026/7ro0_24584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ro0_24584/03_2026/7ro0_24584.map" model { file = "/net/cci-nas-00/data/ceres_data/7ro0_24584/03_2026/7ro0_24584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ro0_24584/03_2026/7ro0_24584.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4426 2.51 5 N 1138 2.21 5 O 1138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6742 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3371 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 19, 'TRANS': 429} Chain: "B" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3371 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 19, 'TRANS': 429} Time building chain proxies: 1.66, per 1000 atoms: 0.25 Number of scatterers: 6742 At special positions: 0 Unit cell: (77, 73.7, 114.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1138 8.00 N 1138 7.00 C 4426 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 178.3 milliseconds 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1568 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 75.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 13 through 25 removed outlier: 3.877A pdb=" N ARG A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 69 removed outlier: 4.474A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL A 41 " --> pdb=" O PHE A 37 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA A 67 " --> pdb=" O GLN A 63 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL A 69 " --> pdb=" O MET A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 101 removed outlier: 4.145A pdb=" N THR A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU A 89 " --> pdb=" O CYS A 85 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 105 removed outlier: 3.853A pdb=" N GLY A 105 " --> pdb=" O PRO A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 102 through 105' Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 127 through 141 removed outlier: 4.779A pdb=" N PHE A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 136 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 141 " --> pdb=" O GLY A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 167 removed outlier: 3.576A pdb=" N GLN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ILE A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN A 157 " --> pdb=" O GLN A 153 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 removed outlier: 3.931A pdb=" N GLY A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 203 removed outlier: 3.843A pdb=" N ILE A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 233 removed outlier: 3.890A pdb=" N ILE A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLY A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N MET A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N MET A 228 " --> pdb=" O MET A 224 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE A 232 " --> pdb=" O MET A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 280 removed outlier: 3.821A pdb=" N ILE A 257 " --> pdb=" O TRP A 253 " (cutoff:3.500A) Proline residue: A 267 - end of helix removed outlier: 4.330A pdb=" N ASP A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 306 removed outlier: 3.656A pdb=" N LEU A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N CYS A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 319 removed outlier: 4.089A pdb=" N LEU A 319 " --> pdb=" O GLY A 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 316 through 319' Processing helix chain 'A' and resid 320 through 325 removed outlier: 4.225A pdb=" N ALA A 325 " --> pdb=" O PRO A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 348 removed outlier: 3.772A pdb=" N PHE A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A 346 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 376 removed outlier: 3.714A pdb=" N THR A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.705A pdb=" N TYR A 382 " --> pdb=" O PHE A 379 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS A 383 " --> pdb=" O PRO A 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 379 through 383' Processing helix chain 'A' and resid 387 through 393 removed outlier: 3.685A pdb=" N ILE A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 401 removed outlier: 4.611A pdb=" N LEU A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU A 398 " --> pdb=" O MET A 394 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA A 399 " --> pdb=" O GLY A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 417 Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 421 through 437 removed outlier: 4.152A pdb=" N THR A 433 " --> pdb=" O GLY A 429 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 458 removed outlier: 4.124A pdb=" N ALA A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A 456 " --> pdb=" O THR A 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 27 removed outlier: 3.953A pdb=" N ARG B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 24 " --> pdb=" O GLN B 20 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU B 27 " --> pdb=" O ARG B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 48 removed outlier: 3.745A pdb=" N MET B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ALA B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 41 " --> pdb=" O PHE B 37 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 70 removed outlier: 3.878A pdb=" N GLY B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 68 " --> pdb=" O ARG B 64 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 69 " --> pdb=" O MET B 65 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS B 70 " --> pdb=" O GLY B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 101 removed outlier: 4.264A pdb=" N SER B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU B 89 " --> pdb=" O CYS B 85 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 116 Processing helix chain 'B' and resid 127 through 141 removed outlier: 4.586A pdb=" N PHE B 133 " --> pdb=" O PRO B 129 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU B 136 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY B 137 " --> pdb=" O PHE B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 166 removed outlier: 3.668A pdb=" N GLN B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY B 159 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B 160 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET B 161 " --> pdb=" O ASN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 191 removed outlier: 3.701A pdb=" N HIS B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA B 179 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 203 removed outlier: 3.821A pdb=" N LEU B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 233 removed outlier: 4.772A pdb=" N GLY B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE B 223 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N MET B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N MET B 228 " --> pdb=" O MET B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 285 removed outlier: 3.802A pdb=" N ILE B 257 " --> pdb=" O TRP B 253 " (cutoff:3.500A) Proline residue: B 267 - end of helix removed outlier: 4.295A pdb=" N LYS B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 306 Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 329 through 349 removed outlier: 3.623A pdb=" N ILE B 342 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 379 removed outlier: 4.246A pdb=" N THR B 365 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL B 374 " --> pdb=" O ALA B 370 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU B 377 " --> pdb=" O MET B 373 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 383 removed outlier: 3.833A pdb=" N HIS B 383 " --> pdb=" O PRO B 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 380 through 383' Processing helix chain 'B' and resid 385 through 394 removed outlier: 4.355A pdb=" N PHE B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 404 through 417 Processing helix chain 'B' and resid 422 through 432 removed outlier: 3.791A pdb=" N LEU B 430 " --> pdb=" O ILE B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 444 through 457 removed outlier: 3.847A pdb=" N LEU B 449 " --> pdb=" O TYR B 445 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.88 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1050 1.31 - 1.43: 1771 1.43 - 1.56: 3991 1.56 - 1.68: 0 1.68 - 1.81: 74 Bond restraints: 6886 Sorted by residual: bond pdb=" C TYR A 75 " pdb=" N PRO A 76 " ideal model delta sigma weight residual 1.335 1.396 -0.062 1.19e-02 7.06e+03 2.68e+01 bond pdb=" C VAL B 127 " pdb=" O VAL B 127 " ideal model delta sigma weight residual 1.237 1.191 0.046 9.80e-03 1.04e+04 2.22e+01 bond pdb=" C TRP B 124 " pdb=" O TRP B 124 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.28e-02 6.10e+03 1.91e+01 bond pdb=" N VAL B 127 " pdb=" CA VAL B 127 " ideal model delta sigma weight residual 1.452 1.486 -0.034 1.18e-02 7.18e+03 8.15e+00 bond pdb=" C ARG B 126 " pdb=" O ARG B 126 " ideal model delta sigma weight residual 1.237 1.209 0.028 1.10e-02 8.26e+03 6.41e+00 ... (remaining 6881 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 9133 2.83 - 5.66: 172 5.66 - 8.49: 32 8.49 - 11.32: 3 11.32 - 14.14: 4 Bond angle restraints: 9344 Sorted by residual: angle pdb=" N VAL B 127 " pdb=" CA VAL B 127 " pdb=" C VAL B 127 " ideal model delta sigma weight residual 112.96 105.66 7.30 1.00e+00 1.00e+00 5.33e+01 angle pdb=" C ARG B 126 " pdb=" N VAL B 127 " pdb=" CA VAL B 127 " ideal model delta sigma weight residual 121.84 116.41 5.43 1.13e+00 7.83e-01 2.31e+01 angle pdb=" C SER A 329 " pdb=" N MET A 330 " pdb=" CA MET A 330 " ideal model delta sigma weight residual 121.54 130.10 -8.56 1.91e+00 2.74e-01 2.01e+01 angle pdb=" C PHE B 166 " pdb=" N ARG B 167 " pdb=" CA ARG B 167 " ideal model delta sigma weight residual 122.46 128.20 -5.74 1.41e+00 5.03e-01 1.66e+01 angle pdb=" CA TRP B 124 " pdb=" C TRP B 124 " pdb=" N TRP B 125 " ideal model delta sigma weight residual 118.08 123.34 -5.26 1.30e+00 5.92e-01 1.64e+01 ... (remaining 9339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.86: 3424 15.86 - 31.72: 449 31.72 - 47.57: 113 47.57 - 63.43: 9 63.43 - 79.29: 7 Dihedral angle restraints: 4002 sinusoidal: 1520 harmonic: 2482 Sorted by residual: dihedral pdb=" CA PHE B 219 " pdb=" C PHE B 219 " pdb=" N ILE B 220 " pdb=" CA ILE B 220 " ideal model delta harmonic sigma weight residual 180.00 151.21 28.79 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ASP B 118 " pdb=" C ASP B 118 " pdb=" N GLN B 119 " pdb=" CA GLN B 119 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA ASP A 118 " pdb=" C ASP A 118 " pdb=" N GLN A 119 " pdb=" CA GLN A 119 " ideal model delta harmonic sigma weight residual 180.00 156.31 23.69 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 3999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 802 0.059 - 0.118: 240 0.118 - 0.176: 48 0.176 - 0.235: 6 0.235 - 0.294: 2 Chirality restraints: 1098 Sorted by residual: chirality pdb=" CA TRP B 124 " pdb=" N TRP B 124 " pdb=" C TRP B 124 " pdb=" CB TRP B 124 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CB THR A 324 " pdb=" CA THR A 324 " pdb=" OG1 THR A 324 " pdb=" CG2 THR A 324 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB ILE A 154 " pdb=" CA ILE A 154 " pdb=" CG1 ILE A 154 " pdb=" CG2 ILE A 154 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1095 not shown) Planarity restraints: 1174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 330 " -0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C MET A 330 " 0.061 2.00e-02 2.50e+03 pdb=" O MET A 330 " -0.023 2.00e-02 2.50e+03 pdb=" N GLY A 331 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 358 " -0.056 5.00e-02 4.00e+02 8.42e-02 1.14e+01 pdb=" N PRO B 359 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO B 359 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 359 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 266 " 0.051 5.00e-02 4.00e+02 7.76e-02 9.63e+00 pdb=" N PRO B 267 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 267 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 267 " 0.042 5.00e-02 4.00e+02 ... (remaining 1171 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 719 2.74 - 3.28: 6401 3.28 - 3.82: 10899 3.82 - 4.36: 12102 4.36 - 4.90: 22058 Nonbonded interactions: 52179 Sorted by model distance: nonbonded pdb=" OE2 GLU B 103 " pdb=" NH2 ARG B 123 " model vdw 2.202 3.120 nonbonded pdb=" OD1 ASN A 270 " pdb=" OG SER A 401 " model vdw 2.302 3.040 nonbonded pdb=" OE1 GLU A 414 " pdb=" OH TYR B 419 " model vdw 2.308 3.040 nonbonded pdb=" OH TYR A 419 " pdb=" OE1 GLU B 414 " model vdw 2.314 3.040 nonbonded pdb=" OD1 ASN A 287 " pdb=" OG1 THR A 289 " model vdw 2.317 3.040 ... (remaining 52174 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.870 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 6886 Z= 0.332 Angle : 1.029 14.144 9344 Z= 0.548 Chirality : 0.059 0.294 1098 Planarity : 0.009 0.084 1174 Dihedral : 14.947 79.288 2434 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.74 % Allowed : 12.43 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.18 (0.19), residues: 894 helix: -3.11 (0.14), residues: 638 sheet: None (None), residues: 0 loop : -3.74 (0.29), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 147 TYR 0.021 0.002 TYR B 419 PHE 0.030 0.002 PHE A 357 TRP 0.034 0.003 TRP A 291 HIS 0.016 0.002 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00767 ( 6886) covalent geometry : angle 1.02882 ( 9344) hydrogen bonds : bond 0.09905 ( 389) hydrogen bonds : angle 5.45448 ( 1167) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8579 (tt) cc_final: 0.8335 (tt) REVERT: A 29 ASP cc_start: 0.8243 (t70) cc_final: 0.7978 (t70) REVERT: A 38 MET cc_start: 0.8859 (mmt) cc_final: 0.8336 (mmt) REVERT: A 165 ILE cc_start: 0.8158 (mm) cc_final: 0.7834 (mt) REVERT: A 298 ILE cc_start: 0.8759 (tt) cc_final: 0.8486 (tt) REVERT: A 332 MET cc_start: 0.7307 (tpt) cc_final: 0.6926 (tpp) REVERT: A 360 MET cc_start: 0.8271 (mtm) cc_final: 0.7956 (mtt) REVERT: B 20 GLN cc_start: 0.8690 (tm-30) cc_final: 0.7763 (tm-30) REVERT: B 54 ASP cc_start: 0.8919 (t0) cc_final: 0.8628 (t0) REVERT: B 75 TYR cc_start: 0.8242 (t80) cc_final: 0.7740 (t80) REVERT: B 113 GLU cc_start: 0.8113 (tt0) cc_final: 0.7854 (tm-30) REVERT: B 279 LEU cc_start: 0.8944 (tp) cc_final: 0.8707 (tp) REVERT: B 391 ILE cc_start: 0.9150 (tp) cc_final: 0.8882 (tp) outliers start: 5 outliers final: 4 residues processed: 137 average time/residue: 0.0891 time to fit residues: 15.8022 Evaluate side-chains 112 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 127 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN B 207 GLN B 418 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.111238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.091794 restraints weight = 10133.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.094671 restraints weight = 5820.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.096684 restraints weight = 4000.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.097969 restraints weight = 3094.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.098886 restraints weight = 2609.803| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6886 Z= 0.126 Angle : 0.595 8.911 9344 Z= 0.297 Chirality : 0.041 0.130 1098 Planarity : 0.006 0.064 1174 Dihedral : 5.474 36.344 966 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.92 % Allowed : 18.20 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.26), residues: 894 helix: -1.32 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -3.35 (0.33), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 282 TYR 0.019 0.001 TYR B 419 PHE 0.020 0.001 PHE A 92 TRP 0.012 0.001 TRP A 291 HIS 0.009 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6886) covalent geometry : angle 0.59514 ( 9344) hydrogen bonds : bond 0.03429 ( 389) hydrogen bonds : angle 4.23787 ( 1167) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.249 Fit side-chains REVERT: A 23 ARG cc_start: 0.7942 (ttp-110) cc_final: 0.7688 (ttm110) REVERT: A 29 ASP cc_start: 0.8290 (t70) cc_final: 0.8069 (t70) REVERT: A 38 MET cc_start: 0.8781 (mmt) cc_final: 0.8066 (mmt) REVERT: A 54 ASP cc_start: 0.9066 (t0) cc_final: 0.8797 (t0) REVERT: A 165 ILE cc_start: 0.8335 (mm) cc_final: 0.8069 (mt) REVERT: A 298 ILE cc_start: 0.8401 (tt) cc_final: 0.8169 (tt) REVERT: A 332 MET cc_start: 0.6810 (tpt) cc_final: 0.6513 (mmt) REVERT: A 360 MET cc_start: 0.8194 (mtm) cc_final: 0.7944 (mtt) REVERT: A 423 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8245 (mt) REVERT: A 430 LEU cc_start: 0.8794 (tp) cc_final: 0.8235 (tt) REVERT: B 20 GLN cc_start: 0.8628 (tm-30) cc_final: 0.7553 (tm-30) REVERT: B 38 MET cc_start: 0.7567 (mmt) cc_final: 0.7359 (mmt) REVERT: B 54 ASP cc_start: 0.8773 (t0) cc_final: 0.8457 (t0) REVERT: B 113 GLU cc_start: 0.7980 (tt0) cc_final: 0.7770 (tm-30) REVERT: B 148 GLU cc_start: 0.8296 (pp20) cc_final: 0.8030 (pp20) REVERT: B 391 ILE cc_start: 0.8928 (tp) cc_final: 0.8656 (tp) outliers start: 13 outliers final: 9 residues processed: 120 average time/residue: 0.0591 time to fit residues: 10.5440 Evaluate side-chains 112 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 350 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 5 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.110211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.090365 restraints weight = 10101.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.093435 restraints weight = 5608.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.095540 restraints weight = 3770.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.096867 restraints weight = 2878.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.097512 restraints weight = 2409.362| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6886 Z= 0.149 Angle : 0.595 8.940 9344 Z= 0.292 Chirality : 0.042 0.129 1098 Planarity : 0.005 0.061 1174 Dihedral : 5.121 33.657 962 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.37 % Allowed : 20.56 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.28), residues: 894 helix: -0.73 (0.21), residues: 650 sheet: None (None), residues: 0 loop : -3.07 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 282 TYR 0.013 0.001 TYR B 419 PHE 0.017 0.001 PHE A 92 TRP 0.011 0.001 TRP A 291 HIS 0.008 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6886) covalent geometry : angle 0.59481 ( 9344) hydrogen bonds : bond 0.03472 ( 389) hydrogen bonds : angle 4.04694 ( 1167) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.259 Fit side-chains REVERT: A 23 ARG cc_start: 0.7987 (ttp-110) cc_final: 0.7604 (ttm-80) REVERT: A 29 ASP cc_start: 0.8270 (t70) cc_final: 0.8054 (t70) REVERT: A 38 MET cc_start: 0.8895 (mmt) cc_final: 0.8323 (mmt) REVERT: A 54 ASP cc_start: 0.9120 (t0) cc_final: 0.8790 (t0) REVERT: A 298 ILE cc_start: 0.8579 (tt) cc_final: 0.8289 (tt) REVERT: A 423 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8285 (mt) REVERT: B 20 GLN cc_start: 0.8653 (tm-30) cc_final: 0.7590 (tm-30) REVERT: B 54 ASP cc_start: 0.8776 (t0) cc_final: 0.8432 (t0) REVERT: B 113 GLU cc_start: 0.7990 (tt0) cc_final: 0.7680 (tm-30) REVERT: B 144 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8849 (p) REVERT: B 148 GLU cc_start: 0.8397 (pp20) cc_final: 0.8067 (pp20) REVERT: B 391 ILE cc_start: 0.9096 (tp) cc_final: 0.8777 (tp) outliers start: 16 outliers final: 13 residues processed: 119 average time/residue: 0.0572 time to fit residues: 10.3649 Evaluate side-chains 118 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 365 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 82 optimal weight: 0.0870 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.111187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.091729 restraints weight = 10084.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.094681 restraints weight = 5804.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.096693 restraints weight = 3977.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.097932 restraints weight = 3077.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.098636 restraints weight = 2602.030| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6886 Z= 0.125 Angle : 0.565 9.041 9344 Z= 0.276 Chirality : 0.041 0.122 1098 Planarity : 0.005 0.058 1174 Dihedral : 4.807 28.624 961 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.11 % Allowed : 21.75 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.29), residues: 894 helix: -0.38 (0.21), residues: 650 sheet: None (None), residues: 0 loop : -2.88 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 98 TYR 0.008 0.001 TYR B 419 PHE 0.015 0.001 PHE A 92 TRP 0.010 0.001 TRP A 291 HIS 0.007 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6886) covalent geometry : angle 0.56532 ( 9344) hydrogen bonds : bond 0.03192 ( 389) hydrogen bonds : angle 3.93186 ( 1167) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.257 Fit side-chains REVERT: A 23 ARG cc_start: 0.7996 (ttp-110) cc_final: 0.7555 (ttm-80) REVERT: A 29 ASP cc_start: 0.8322 (t70) cc_final: 0.8094 (t70) REVERT: A 38 MET cc_start: 0.8863 (mmt) cc_final: 0.8269 (mmt) REVERT: A 54 ASP cc_start: 0.9092 (t0) cc_final: 0.8761 (t0) REVERT: A 298 ILE cc_start: 0.8470 (tt) cc_final: 0.8181 (tt) REVERT: A 423 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8226 (mt) REVERT: B 20 GLN cc_start: 0.8702 (tm-30) cc_final: 0.7543 (tm-30) REVERT: B 54 ASP cc_start: 0.8746 (t0) cc_final: 0.8388 (t0) REVERT: B 113 GLU cc_start: 0.7982 (tt0) cc_final: 0.7592 (tm-30) REVERT: B 125 TRP cc_start: 0.9114 (p90) cc_final: 0.8876 (p90) REVERT: B 144 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8862 (p) REVERT: B 148 GLU cc_start: 0.8376 (pp20) cc_final: 0.8069 (pp20) REVERT: B 391 ILE cc_start: 0.9047 (tp) cc_final: 0.8730 (tp) outliers start: 21 outliers final: 15 residues processed: 121 average time/residue: 0.0552 time to fit residues: 10.1857 Evaluate side-chains 121 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 365 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 6 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 43 optimal weight: 0.0770 chunk 40 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.113148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.093783 restraints weight = 10023.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.096759 restraints weight = 5771.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.098826 restraints weight = 3947.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.100152 restraints weight = 3040.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.101142 restraints weight = 2545.443| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6886 Z= 0.105 Angle : 0.545 9.180 9344 Z= 0.267 Chirality : 0.039 0.121 1098 Planarity : 0.005 0.055 1174 Dihedral : 4.558 25.345 961 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.51 % Allowed : 23.08 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.29), residues: 894 helix: -0.10 (0.22), residues: 648 sheet: None (None), residues: 0 loop : -2.70 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 98 TYR 0.009 0.001 TYR A 419 PHE 0.013 0.001 PHE A 92 TRP 0.009 0.001 TRP A 291 HIS 0.005 0.000 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6886) covalent geometry : angle 0.54502 ( 9344) hydrogen bonds : bond 0.02941 ( 389) hydrogen bonds : angle 3.79179 ( 1167) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.245 Fit side-chains REVERT: A 22 ILE cc_start: 0.8311 (tt) cc_final: 0.8086 (tt) REVERT: A 23 ARG cc_start: 0.8008 (ttp-110) cc_final: 0.7573 (ttm-80) REVERT: A 29 ASP cc_start: 0.8310 (t70) cc_final: 0.8082 (t70) REVERT: A 38 MET cc_start: 0.8840 (mmt) cc_final: 0.8243 (mmt) REVERT: A 54 ASP cc_start: 0.9100 (t0) cc_final: 0.8756 (t0) REVERT: A 298 ILE cc_start: 0.8302 (tt) cc_final: 0.8010 (tt) REVERT: A 328 PHE cc_start: 0.7015 (OUTLIER) cc_final: 0.6761 (m-10) REVERT: A 422 ILE cc_start: 0.8606 (tp) cc_final: 0.8322 (tp) REVERT: B 20 GLN cc_start: 0.8699 (tm-30) cc_final: 0.7812 (tm-30) REVERT: B 54 ASP cc_start: 0.8682 (t0) cc_final: 0.8313 (t0) REVERT: B 113 GLU cc_start: 0.7928 (tt0) cc_final: 0.7624 (tm-30) REVERT: B 125 TRP cc_start: 0.9024 (p90) cc_final: 0.8788 (p90) REVERT: B 136 LEU cc_start: 0.8401 (tp) cc_final: 0.8085 (tp) REVERT: B 144 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.8850 (p) REVERT: B 148 GLU cc_start: 0.8357 (pp20) cc_final: 0.8106 (pp20) REVERT: B 391 ILE cc_start: 0.8972 (tp) cc_final: 0.8674 (tp) outliers start: 17 outliers final: 13 residues processed: 128 average time/residue: 0.0541 time to fit residues: 10.6047 Evaluate side-chains 119 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 328 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 54 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 34 optimal weight: 0.3980 chunk 81 optimal weight: 0.3980 chunk 67 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.113507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.093789 restraints weight = 10039.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.096888 restraints weight = 5690.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.098958 restraints weight = 3849.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.100444 restraints weight = 2943.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.101414 restraints weight = 2430.802| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6886 Z= 0.104 Angle : 0.540 9.115 9344 Z= 0.262 Chirality : 0.039 0.122 1098 Planarity : 0.005 0.054 1174 Dihedral : 4.415 25.388 961 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.55 % Allowed : 23.22 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.29), residues: 894 helix: 0.09 (0.22), residues: 648 sheet: None (None), residues: 0 loop : -2.56 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 98 TYR 0.007 0.001 TYR A 419 PHE 0.012 0.001 PHE A 92 TRP 0.009 0.001 TRP A 291 HIS 0.005 0.000 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6886) covalent geometry : angle 0.54021 ( 9344) hydrogen bonds : bond 0.02894 ( 389) hydrogen bonds : angle 3.74248 ( 1167) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.220 Fit side-chains REVERT: A 29 ASP cc_start: 0.8244 (t70) cc_final: 0.8043 (t70) REVERT: A 38 MET cc_start: 0.8881 (mmt) cc_final: 0.8268 (mmt) REVERT: A 298 ILE cc_start: 0.8377 (tt) cc_final: 0.8042 (tt) REVERT: A 328 PHE cc_start: 0.6903 (OUTLIER) cc_final: 0.6607 (m-10) REVERT: A 422 ILE cc_start: 0.8595 (tp) cc_final: 0.8350 (tp) REVERT: B 20 GLN cc_start: 0.8639 (tm-30) cc_final: 0.7753 (tm-30) REVERT: B 54 ASP cc_start: 0.8694 (t0) cc_final: 0.8307 (t0) REVERT: B 113 GLU cc_start: 0.7970 (tt0) cc_final: 0.7583 (tm-30) REVERT: B 136 LEU cc_start: 0.8426 (tp) cc_final: 0.8104 (tp) REVERT: B 144 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8837 (p) REVERT: B 357 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7287 (m-80) REVERT: B 391 ILE cc_start: 0.9060 (tp) cc_final: 0.8705 (tp) REVERT: B 416 THR cc_start: 0.9430 (m) cc_final: 0.9175 (m) outliers start: 24 outliers final: 16 residues processed: 128 average time/residue: 0.0549 time to fit residues: 10.7622 Evaluate side-chains 125 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 357 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 0.0470 chunk 86 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.112443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.092854 restraints weight = 9989.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.095579 restraints weight = 6104.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.097457 restraints weight = 4365.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.098486 restraints weight = 3475.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.099587 restraints weight = 3018.465| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6886 Z= 0.128 Angle : 0.562 8.967 9344 Z= 0.274 Chirality : 0.041 0.120 1098 Planarity : 0.005 0.055 1174 Dihedral : 4.442 25.582 961 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.96 % Allowed : 23.96 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.29), residues: 894 helix: 0.17 (0.22), residues: 648 sheet: None (None), residues: 0 loop : -2.53 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 98 TYR 0.036 0.001 TYR B 419 PHE 0.012 0.001 PHE A 92 TRP 0.012 0.001 TRP B 125 HIS 0.006 0.000 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6886) covalent geometry : angle 0.56243 ( 9344) hydrogen bonds : bond 0.03113 ( 389) hydrogen bonds : angle 3.76196 ( 1167) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.253 Fit side-chains REVERT: A 29 ASP cc_start: 0.8240 (t70) cc_final: 0.7933 (t70) REVERT: A 38 MET cc_start: 0.8884 (mmt) cc_final: 0.8280 (mmt) REVERT: A 298 ILE cc_start: 0.8354 (tt) cc_final: 0.8048 (tt) REVERT: A 422 ILE cc_start: 0.8729 (tp) cc_final: 0.8493 (tp) REVERT: B 54 ASP cc_start: 0.8748 (t0) cc_final: 0.8397 (t0) REVERT: B 113 GLU cc_start: 0.7978 (tt0) cc_final: 0.7514 (tm-30) REVERT: B 136 LEU cc_start: 0.8487 (tp) cc_final: 0.8117 (tp) REVERT: B 144 VAL cc_start: 0.9104 (OUTLIER) cc_final: 0.8895 (p) REVERT: B 391 ILE cc_start: 0.9158 (tp) cc_final: 0.8707 (tp) outliers start: 20 outliers final: 15 residues processed: 123 average time/residue: 0.0506 time to fit residues: 9.5040 Evaluate side-chains 123 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 328 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.112756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.093057 restraints weight = 10087.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.096098 restraints weight = 5709.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.098120 restraints weight = 3885.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.099461 restraints weight = 2987.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.100489 restraints weight = 2499.382| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6886 Z= 0.120 Angle : 0.574 10.170 9344 Z= 0.276 Chirality : 0.040 0.123 1098 Planarity : 0.005 0.054 1174 Dihedral : 4.392 26.353 960 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.25 % Allowed : 24.26 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.29), residues: 894 helix: 0.24 (0.22), residues: 646 sheet: None (None), residues: 0 loop : -2.39 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 23 TYR 0.032 0.001 TYR B 419 PHE 0.012 0.001 PHE B 379 TRP 0.010 0.001 TRP A 291 HIS 0.006 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6886) covalent geometry : angle 0.57423 ( 9344) hydrogen bonds : bond 0.03023 ( 389) hydrogen bonds : angle 3.75135 ( 1167) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.341 Fit side-chains REVERT: A 29 ASP cc_start: 0.8196 (t70) cc_final: 0.7932 (t70) REVERT: A 38 MET cc_start: 0.8909 (mmt) cc_final: 0.8292 (mmt) REVERT: A 294 MET cc_start: 0.7623 (tmm) cc_final: 0.6780 (tmm) REVERT: A 298 ILE cc_start: 0.8607 (tt) cc_final: 0.8212 (tt) REVERT: A 422 ILE cc_start: 0.8790 (tp) cc_final: 0.8563 (tp) REVERT: B 54 ASP cc_start: 0.8754 (t0) cc_final: 0.8405 (t0) REVERT: B 144 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8889 (p) REVERT: B 148 GLU cc_start: 0.8643 (pp20) cc_final: 0.8390 (tm-30) REVERT: B 391 ILE cc_start: 0.9195 (tp) cc_final: 0.8743 (tp) outliers start: 22 outliers final: 18 residues processed: 124 average time/residue: 0.0555 time to fit residues: 10.5066 Evaluate side-chains 122 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 357 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 30 optimal weight: 0.0670 chunk 20 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.114416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.094385 restraints weight = 10003.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.097366 restraints weight = 5878.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.099299 restraints weight = 4087.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.100806 restraints weight = 3208.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.101656 restraints weight = 2693.700| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6886 Z= 0.103 Angle : 0.576 11.795 9344 Z= 0.271 Chirality : 0.040 0.258 1098 Planarity : 0.005 0.053 1174 Dihedral : 4.248 26.789 960 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.66 % Allowed : 25.44 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.30), residues: 894 helix: 0.38 (0.22), residues: 644 sheet: None (None), residues: 0 loop : -2.24 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 23 TYR 0.035 0.001 TYR B 419 PHE 0.010 0.001 PHE A 92 TRP 0.009 0.001 TRP B 125 HIS 0.005 0.000 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 6886) covalent geometry : angle 0.57599 ( 9344) hydrogen bonds : bond 0.02823 ( 389) hydrogen bonds : angle 3.70263 ( 1167) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.254 Fit side-chains REVERT: A 29 ASP cc_start: 0.8190 (t70) cc_final: 0.7954 (t70) REVERT: A 38 MET cc_start: 0.8867 (mmt) cc_final: 0.8235 (mmt) REVERT: A 294 MET cc_start: 0.7582 (tmm) cc_final: 0.6731 (tmm) REVERT: A 298 ILE cc_start: 0.8521 (tt) cc_final: 0.8127 (tt) REVERT: A 422 ILE cc_start: 0.8650 (tp) cc_final: 0.8420 (tp) REVERT: B 54 ASP cc_start: 0.8677 (t0) cc_final: 0.8271 (t0) REVERT: B 144 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8866 (p) REVERT: B 148 GLU cc_start: 0.8558 (pp20) cc_final: 0.8301 (tm-30) REVERT: B 218 VAL cc_start: 0.7821 (p) cc_final: 0.7576 (p) REVERT: B 228 MET cc_start: 0.7354 (mmt) cc_final: 0.7138 (mmm) REVERT: B 391 ILE cc_start: 0.9104 (tp) cc_final: 0.8812 (tp) outliers start: 18 outliers final: 15 residues processed: 123 average time/residue: 0.0492 time to fit residues: 9.2782 Evaluate side-chains 120 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 357 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 77 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.114288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.095480 restraints weight = 9966.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.098266 restraints weight = 6013.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.100014 restraints weight = 4249.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.101396 restraints weight = 3368.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.102238 restraints weight = 2846.128| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6886 Z= 0.110 Angle : 0.591 11.244 9344 Z= 0.280 Chirality : 0.041 0.229 1098 Planarity : 0.005 0.053 1174 Dihedral : 4.226 26.960 960 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.96 % Allowed : 25.44 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.30), residues: 894 helix: 0.42 (0.22), residues: 646 sheet: None (None), residues: 0 loop : -2.19 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 23 TYR 0.033 0.001 TYR B 419 PHE 0.022 0.001 PHE B 379 TRP 0.009 0.001 TRP A 291 HIS 0.005 0.000 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 6886) covalent geometry : angle 0.59092 ( 9344) hydrogen bonds : bond 0.02872 ( 389) hydrogen bonds : angle 3.68184 ( 1167) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.279 Fit side-chains REVERT: A 29 ASP cc_start: 0.8220 (t70) cc_final: 0.7999 (t70) REVERT: A 38 MET cc_start: 0.8896 (mmt) cc_final: 0.8270 (mmt) REVERT: A 294 MET cc_start: 0.7642 (tmm) cc_final: 0.6796 (tmm) REVERT: A 298 ILE cc_start: 0.8565 (tt) cc_final: 0.8173 (tt) REVERT: A 422 ILE cc_start: 0.8720 (tp) cc_final: 0.8493 (tp) REVERT: B 54 ASP cc_start: 0.8742 (t0) cc_final: 0.8371 (t0) REVERT: B 75 TYR cc_start: 0.8527 (t80) cc_final: 0.8233 (t80) REVERT: B 148 GLU cc_start: 0.8575 (pp20) cc_final: 0.8340 (tm-30) REVERT: B 391 ILE cc_start: 0.9152 (tp) cc_final: 0.8721 (tp) outliers start: 20 outliers final: 16 residues processed: 125 average time/residue: 0.0506 time to fit residues: 9.6825 Evaluate side-chains 122 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 357 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 31 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 0.1980 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.114156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.094117 restraints weight = 10007.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.097036 restraints weight = 5898.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.099133 restraints weight = 4106.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.100217 restraints weight = 3203.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.101323 restraints weight = 2748.315| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6886 Z= 0.116 Angle : 0.612 13.434 9344 Z= 0.287 Chirality : 0.041 0.212 1098 Planarity : 0.005 0.054 1174 Dihedral : 4.233 27.037 960 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.51 % Allowed : 26.33 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.30), residues: 894 helix: 0.50 (0.22), residues: 644 sheet: None (None), residues: 0 loop : -2.29 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 23 TYR 0.039 0.001 TYR B 419 PHE 0.011 0.001 PHE A 92 TRP 0.010 0.001 TRP A 291 HIS 0.005 0.000 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6886) covalent geometry : angle 0.61171 ( 9344) hydrogen bonds : bond 0.02932 ( 389) hydrogen bonds : angle 3.69411 ( 1167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1012.04 seconds wall clock time: 18 minutes 7.94 seconds (1087.94 seconds total)